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MIC-DKFZ / BraTS2017

Apache License 2.0
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Too few informations in readme leads to many mistakes #13

Closed samieti02 closed 6 years ago

samieti02 commented 6 years ago

Hi dear Sir,

I've spent a lot of time trying to run the code, but without success. I always get mistakes. In fact: The first one was about downsample. To solve it, i uploaded the lasagne package like this

pip install --upgrade https://github.com/Lasagne/Lasagne/archive/master.zip

Then the next one was an ImportError refering to this line code

#from sklearn.cross_validation import KFold # this is deprecated -> bad, but need to keep it here for reproducibility

If you know that a line code is deprecated, why do you keep it in the code? This is really annoying. I have change the line code like

from sklearn.model_selection import KFold,

Hoping that it will not cause more mistakes

Then the next one was an error module about SimpleITK. I solved it with the following code conda install -c https://conda.anaconda.org/simpleitk SimpleITK

Then i enter the command "python train_network.py 0", and i got the error

raise IOError("%s not found." % path)
IOError: ../../BraTS17TrainingPre\id_name_conversion.txt not found.

I thought, maybe I should first execute the command "python run_preprocessing -m train", then i got

(brats_dkfz) C:\Users\me\BraTS2017_master>python run_preprocessing -m train
python: can't open file 'run_preprocessing': [Errno 2] No such file or directory

And i am in the good file (brats_dkfz) C:\Users\me\BraTS2017_master\paths.py
\predict_test_set.py
\predict_val_set.py \run_preprocessing.py ....

I create a python 2.7 environment in anaconda with all the depencies, and also the batchgenerators.

Since I'm not an expert in Python, I don't know what to do anymore, how to proceed. And I have to get the approach going, for further tests. Can you please help me?

Thanks

FabianIsensee commented 6 years ago

Hi,

If you know that a line code is deprecated, why do you keep it in the code? This is really annoying. I have change the line code like

Like I said in the comment: this is because I used it once a while back and wanted to keep the folds the same throughout my experiments so that I would be able to compare them properly. I know this is not ideal, but that was the way I did it back then. You must downgrade your version of sklearn and it will work again (pip install sklearn==some_version_number). Your workaround does not work because the new KFold works differently.

The file id_name_conversion.txt is created during preprocessing. You need to add the .py file extension to your command for it to work C:\Users\me\BraTS2017_master>python run_preprocessing.py -m train. As the error message said: there is no file named run_preprocessing.

You will not be able to run the training however. Windows is not supported by batchgenerators because python multithreading on windows is broken. All my repos were tested on ubuntu only.

I hope this helps! Fabian